Analysis module 4: 16S vs ORV outcome (BM samples with strict filtering) RoVI study — 24 February, 2022

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Sample summary

Alpha diversity

Beta diversity

Differential taxa

Summary figures

Longitudinal abundance comparisons

Session info

Sample summary

Input data: breastmilk samples (BM1, BM2, BM3)

  • n samples = 1124
  • n taxa: genera = 350; variants = 1712
  • n taxa (rarefied): genera = 349; variants = 1711

Statistical methods for mixed-effects models

  • Linear mixed-effects models fit with family ID as a random effect
  • Association with ORV outcome determined by comparing fit of model with country/age vs model with age alone

Alpha diversity

Column

Seroconversion

Longitudinal plots - Shannon

Longitudinal plots - richness

Blue = seroconversion+, Orange = seroconversion-.

N by country

, ,  = IND

   
    BM1 BM2 BM3
  0 193 175 168
  1  79  70  62

, ,  = MLW

   
    BM1 BM2 BM3
  0  61  54  56
  1  19  16  11

, ,  = UK

   
    BM1 BM2 BM3
  0  21  16  18
  1  21  18  15

, ,  = IND (neo+)

   
    BM1 BM2 BM3
  0 102  90  91
  1  47  42  35

, ,  = IND (neo-)

   
    BM1 BM2 BM3
  0  90  84  76
  1  32  28  27

P values, cross-sectional analayses - Shannon

   variable n total (r) responders non-responders      RR (95% CI)       p
1   Shannon    272 (79)  1.8 (0.6)      1.8 (0.6) 0.95 (0.67-1.29) 0.77009
2   Shannon    245 (70)  2.1 (0.6)      2.0 (0.5) 1.14 (0.79-1.57) 0.46842
3   Shannon    230 (62)  2.0 (0.5)      2.0 (0.5) 0.85 (0.53-1.27) 0.44584
4   Shannon     80 (19)  1.9 (0.6)      1.7 (0.7) 1.37 (0.78-2.16) 0.25498
5   Shannon     70 (16)  1.5 (0.5)      1.9 (0.5) 0.23 (0.06-0.69) 0.01119
6   Shannon     67 (11)  1.9 (0.5)      1.8 (0.5) 1.36 (0.47-3.00) 0.53177
7   Shannon     42 (21)  1.2 (0.4)      1.2 (0.5) 1.08 (0.48-1.63) 0.80502
8   Shannon     34 (18)  1.4 (0.5)      1.4 (0.6) 0.97 (0.41-1.50) 0.91999
9   Shannon     33 (15)  1.4 (0.5)      1.5 (0.6) 0.78 (0.29-1.41) 0.49574
10  Shannon    149 (47)  1.8 (0.6)      1.8 (0.6) 1.01 (0.65-1.46) 0.95330
11  Shannon    132 (42)  2.1 (0.6)      2.0 (0.5) 1.40 (0.93-1.93) 0.10919
12  Shannon    126 (35)  1.9 (0.5)      2.0 (0.5) 0.88 (0.46-1.48) 0.64841
13  Shannon    122 (32)  1.8 (0.6)      1.8 (0.6) 0.87 (0.49-1.42) 0.60958
14  Shannon    112 (28)  2.0 (0.5)      2.1 (0.5) 0.78 (0.37-1.44) 0.45902
15  Shannon    103 (27)  2.1 (0.5)      2.1 (0.5) 0.84 (0.40-1.52) 0.59319
        country sample
1         India    BM1
2         India    BM2
3         India    BM3
4        Malawi    BM1
5        Malawi    BM2
6        Malawi    BM3
7            UK    BM1
8            UK    BM2
9            UK    BM3
10 India (neo+)    BM1
11 India (neo+)    BM2
12 India (neo+)    BM3
13 India (neo-)    BM1
14 India (neo-)    BM2
15 India (neo-)    BM3

P values, cross-sectional analayses - richness

   variable n total (r)  responders non-responders      RR (95% CI)       p
1  Observed    272 (79) 27.1 (11.8)    26.5 (11.5) 1.07 (0.69-1.55) 0.73646
2  Observed    245 (70)  28.4 (9.4)    26.6 (10.9) 1.45 (0.92-2.08) 0.10866
3  Observed    230 (62)  25.9 (8.4)     25.4 (9.4) 1.19 (0.68-1.88) 0.52412
4  Observed     80 (19) 25.7 (11.6)    23.4 (12.7) 1.35 (0.67-2.39) 0.39364
5  Observed     70 (16)  21.3 (9.9)    25.4 (11.1) 0.43 (0.11-1.26) 0.14496
6  Observed     67 (11) 28.6 (10.9)    26.1 (10.6) 1.66 (0.42-4.15) 0.44668
7  Observed     42 (21)  12.2 (4.6)     12.7 (7.2) 1.01 (0.43-1.58) 0.98400
8  Observed     34 (18)  14.7 (6.9)     18.4 (8.2) 0.45 (0.08-1.09) 0.13654
9  Observed     33 (15)  14.6 (4.8)     16.6 (7.1) 0.77 (0.19-1.64) 0.61304
10 Observed    149 (47) 27.9 (12.1)    25.5 (11.3) 1.36 (0.82-1.98) 0.22406
11 Observed    132 (42)  29.4 (9.7)    26.2 (11.1) 1.71 (1.02-2.40) 0.05182
12 Observed    126 (35)  25.9 (7.8)     24.6 (9.6) 1.48 (0.71-2.44) 0.27074
13 Observed    122 (32) 26.1 (11.5)    27.5 (11.7) 0.75 (0.34-1.44) 0.42038
14 Observed    112 (28)  27.0 (9.0)    27.1 (10.8) 1.06 (0.45-2.07) 0.87477
15 Observed    103 (27)  25.8 (9.3)     26.1 (9.1) 0.95 (0.40-1.92) 0.90272
        country sample
1         India    BM1
2         India    BM2
3         India    BM3
4        Malawi    BM1
5        Malawi    BM2
6        Malawi    BM3
7            UK    BM1
8            UK    BM2
9            UK    BM3
10 India (neo+)    BM1
11 India (neo+)    BM2
12 India (neo+)    BM3
13 India (neo-)    BM1
14 India (neo-)    BM2
15 India (neo-)    BM3

P values, longitudinal mixed-effects models

           Shannon log(Observed)
IND         0.8925        0.1791
IND (neo+)  0.4638        0.0192
IND (neo-)  0.3305        0.6376
MLW         0.8113        0.8196
UK          0.7774        0.3284

Post-ORV RV-IgA

Week of life 1

Correlation coefficients values
                India India_exposed India_unexposed Malawi      UK
Shannon       -0.0757       -0.0575         -0.1209 0.0783  0.1141
log(richness) -0.0925       -0.0533         -0.1123 0.0677 -0.0341
P values
               India India_exposed India_unexposed Malawi     UK
Shannon       0.2133        0.4859          0.1847 0.4899 0.4553
log(richness) 0.1282        0.5185          0.2180 0.5505 0.8240
N
  India India_neo_pos India_neo_neg Malawi UK
1   272           149           122     80 45
2   272           149           122     80 45

Week of life 7

Correlation coefficients values
                India India_exposed India_unexposed  Malawi      UK
Shannon       -0.0753       -0.0526         -0.0748 -0.1939  0.1138
log(richness)  0.0131        0.0151          0.0237 -0.1916 -0.2508
P values
               India India_exposed India_unexposed Malawi     UK
Shannon       0.2400        0.5490          0.4333 0.1078 0.5025
log(richness) 0.8383        0.8639          0.8039 0.1121 0.1343
N
  India India_neo_pos India_neo_neg Malawi UK
1   245           132           112     70 37
2   245           132           112     70 37

Week of life 11

Correlation coefficients values
                India India_exposed India_unexposed Malawi      UK
Shannon       -0.1097       -0.0566         -0.0118 0.0720 -0.1496
log(richness)  0.0248        0.0776          0.0603 0.0927 -0.1911
P values
               India India_exposed India_unexposed Malawi     UK
Shannon       0.0969        0.5289          0.9062 0.5625 0.3840
log(richness) 0.7086        0.3875          0.5453 0.4554 0.2642
N
  India India_neo_pos India_neo_neg Malawi UK
1   230           126           103     67 36
2   230           126           103     67 36

Dose 1 shedding

Longitudinal plots - Shannon

Longitudinal plots - richness

N by country

, ,  = IND

   
    BM1 BM2
  0 195 177
  1  77  68

, ,  = MLW

   
    BM1 BM2
  0  35  32
  1  42  35

, ,  = UK

   
    BM1 BM2
  0   0   0
  1   0   0

, ,  = IND (neo+)

   
    BM1 BM2
  0 119 106
  1  28  24

, ,  = IND (neo-)

   
    BM1 BM2
  0  74  69
  1  48  43

P values, cross-sectional analayses - Shannon

   variable n total (r) responders non-responders      RR (95% CI)       p
1   Shannon    272 (77)  1.9 (0.6)      1.8 (0.6) 1.28 (0.93-1.67) 0.12292
2   Shannon    245 (68)  2.1 (0.5)      2.0 (0.5) 1.26 (0.88-1.72) 0.19800
3   Shannon       0 (0)       <NA>           <NA>             <NA>    <NA>
4   Shannon     77 (42)  1.7 (0.6)      1.9 (0.7) 0.83 (0.54-1.13) 0.27120
5   Shannon     67 (35)  1.8 (0.5)      1.8 (0.6) 0.99 (0.60-1.37) 0.95574
6   Shannon       0 (0)       <NA>           <NA>             <NA>    <NA>
7   Shannon       0 (0)       <NA>           <NA>             <NA>    <NA>
8   Shannon       0 (0)       <NA>           <NA>             <NA>    <NA>
9   Shannon       0 (0)       <NA>           <NA>             <NA>    <NA>
10  Shannon    147 (28)  1.9 (0.6)      1.8 (0.6) 1.19 (0.66-1.96) 0.54339
11  Shannon    130 (24)  2.1 (0.6)      2.0 (0.6) 1.30 (0.69-2.25) 0.40581
12  Shannon       0 (0)       <NA>           <NA>             <NA>    <NA>
13  Shannon    122 (48)  1.9 (0.6)      1.8 (0.6) 1.30 (0.91-1.70) 0.14532
14  Shannon    112 (43)  2.1 (0.5)      2.0 (0.5) 1.24 (0.78-1.73) 0.32884
15  Shannon       0 (0)       <NA>           <NA>             <NA>    <NA>
        country sample
1         India    BM1
2         India    BM2
3         India    BM3
4        Malawi    BM1
5        Malawi    BM2
6        Malawi    BM3
7            UK    BM1
8            UK    BM2
9            UK    BM3
10 India (neo+)    BM1
11 India (neo+)    BM2
12 India (neo+)    BM3
13 India (neo-)    BM1
14 India (neo-)    BM2
15 India (neo-)    BM3

P values, cross-sectional analayses - richness

   variable n total (r)  responders non-responders      RR (95% CI)       p
1  Observed    272 (77) 29.5 (12.4)    25.4 (11.0) 1.61 (1.11-2.16) 0.01735
2  Observed    245 (68)  27.2 (9.5)    27.1 (10.9) 1.10 (0.66-1.69) 0.69248
3  Observed       0 (0)        <NA>           <NA>             <NA>    <NA>
4  Observed     77 (42) 22.5 (11.6)    25.6 (12.2) 0.74 (0.39-1.11) 0.17996
5  Observed     67 (35) 25.5 (13.0)    23.9 (10.7) 1.08 (0.60-1.51) 0.74364
6  Observed       0 (0)        <NA>           <NA>             <NA>    <NA>
7  Observed       0 (0)        <NA>           <NA>             <NA>    <NA>
8  Observed       0 (0)        <NA>           <NA>             <NA>    <NA>
9  Observed       0 (0)        <NA>           <NA>             <NA>    <NA>
10 Observed    147 (28) 28.4 (13.3)    25.6 (11.1) 1.39 (0.66-2.54) 0.37163
11 Observed    130 (24)  27.2 (9.9)    27.2 (10.9) 1.12 (0.46-2.38) 0.78807
12 Observed       0 (0)        <NA>           <NA>             <NA>    <NA>
13 Observed    122 (48) 30.4 (12.0)    25.1 (10.9) 1.63 (1.10-2.08) 0.02291
14 Observed    112 (43)  27.3 (9.4)    27.0 (11.0) 1.11 (0.59-1.72) 0.71270
15 Observed       0 (0)        <NA>           <NA>             <NA>    <NA>
        country sample
1         India    BM1
2         India    BM2
3         India    BM3
4        Malawi    BM1
5        Malawi    BM2
6        Malawi    BM3
7            UK    BM1
8            UK    BM2
9            UK    BM3
10 India (neo+)    BM1
11 India (neo+)    BM2
12 India (neo+)    BM3
13 India (neo-)    BM1
14 India (neo-)    BM2
15 India (neo-)    BM3

P values, longitudinal mixed-effects models

           Shannon log(Observed)
IND         0.0623        0.0503
IND (neo+)  0.3340        0.3866
IND (neo-)  0.1005        0.0583
MLW         0.3646        0.3763

Beta diversity

Column

Unweighted

Seroconversion

                    R2     p   n    country week full        outcome
IND_BM1      0.3788083 0.384 272        IND    1    1 seroconversion
IND_BM2      0.4746925 0.269 245        IND    7    1 seroconversion
IND_BM3      0.3475465 0.752 230        IND   11    1 seroconversion
MLW_BM1      1.2432429 0.455  80        MLW    1    1 seroconversion
MLW_BM2      1.8015592 0.174  70        MLW    7    1 seroconversion
MLW_BM3      0.9029032 0.932  67        MLW   11    1 seroconversion
UK_BM1       1.7106198 0.794  42         UK    1    1 seroconversion
UK_BM2       4.3098177 0.114  34         UK    7    1 seroconversion
UK_BM3       1.7661924 0.887  33         UK   11    1 seroconversion
INDexp_BM1   0.7405885 0.283 149 IND (neo+)    1    0 seroconversion
INDexp_BM2   0.8373905 0.306 132 IND (neo+)    7    0 seroconversion
INDexp_BM3   0.5392045 0.881 126 IND (neo+)   11    0 seroconversion
INDunexp_BM1 0.6115097 0.825 122 IND (neo-)    1    0 seroconversion
INDunexp_BM2 0.6878895 0.816 112 IND (neo-)    7    0 seroconversion
INDunexp_BM3 1.3375167 0.101 103 IND (neo-)   11    0 seroconversion

RV-IgA

                    R2     p   n    country week full           outcome
IND_BM1      0.5008963 0.096 272        IND    1    1 RV-IgA (post-ORV)
IND_BM2      0.5394922 0.149 245        IND    7    1 RV-IgA (post-ORV)
IND_BM3      0.4191227 0.530 230        IND   11    1 RV-IgA (post-ORV)
MLW_BM1      0.9926848 0.734  80        MLW    1    1 RV-IgA (post-ORV)
MLW_BM2      2.0630760 0.093  70        MLW    7    1 RV-IgA (post-ORV)
MLW_BM3      0.7910595 0.965  67        MLW   11    1 RV-IgA (post-ORV)
UK_BM1       2.2612923 0.465  45         UK    1    1 RV-IgA (post-ORV)
UK_BM2       5.9977991 0.005  37         UK    7    1 RV-IgA (post-ORV)
UK_BM3       2.7042128 0.486  36         UK   11    1 RV-IgA (post-ORV)
INDexp_BM1   0.7849895 0.265 149 IND (neo+)    1    0 RV-IgA (post-ORV)
INDexp_BM2   0.6647328 0.646 132 IND (neo+)    7    0 RV-IgA (post-ORV)
INDexp_BM3   0.6365908 0.752 126 IND (neo+)   11    0 RV-IgA (post-ORV)
INDunexp_BM1 0.6382606 0.789 122 IND (neo-)    1    0 RV-IgA (post-ORV)
INDunexp_BM2 0.9788583 0.349 112 IND (neo-)    7    0 RV-IgA (post-ORV)
INDunexp_BM3 1.2387376 0.150 103 IND (neo-)   11    0 RV-IgA (post-ORV)

Dose 1 shedding

                    R2     p   n    country week full         outcome
IND_BM1      0.4633303 0.166 272        IND    1    1 dose 1 shedding
IND_BM2      0.3745513 0.592 245        IND    7    1 dose 1 shedding
MLW_BM1      1.6554250 0.190  77        MLW    1    1 dose 1 shedding
MLW_BM2      1.0958493 0.793  67        MLW    7    1 dose 1 shedding
INDexp_BM1   0.3271173 0.991 147 IND (neo+)    1    0 dose 1 shedding
INDexp_BM2   0.6294284 0.728 130 IND (neo+)    7    0 dose 1 shedding
INDunexp_BM1 1.2889788 0.036 122 IND (neo-)    1    0 dose 1 shedding
INDunexp_BM2 0.7920155 0.649 112 IND (neo-)    7    0 dose 1 shedding

Weighted

Seroconversion

                    R2     p   n    country week full        outcome
IND_BM1      0.4073267 0.330 272        IND    1    1 seroconversion
IND_BM2      0.3559273 0.521 245        IND    7    1 seroconversion
IND_BM3      0.5876315 0.160 230        IND   11    1 seroconversion
MLW_BM1      0.8355983 0.816  80        MLW    1    1 seroconversion
MLW_BM2      3.0451683 0.022  70        MLW    7    1 seroconversion
MLW_BM3      0.5401890 0.975  67        MLW   11    1 seroconversion
UK_BM1       2.6524856 0.312  42         UK    1    1 seroconversion
UK_BM2       3.6408664 0.282  34         UK    7    1 seroconversion
UK_BM3       1.5260302 0.883  33         UK   11    1 seroconversion
INDexp_BM1   0.3559372 0.850 149 IND (neo+)    1    0 seroconversion
INDexp_BM2   0.5027904 0.743 132 IND (neo+)    7    0 seroconversion
INDexp_BM3   1.0114751 0.230 126 IND (neo+)   11    0 seroconversion
INDunexp_BM1 2.6860734 0.007 122 IND (neo-)    1    0 seroconversion
INDunexp_BM2 0.8562030 0.449 112 IND (neo-)    7    0 seroconversion
INDunexp_BM3 0.6743814 0.740 103 IND (neo-)   11    0 seroconversion

RV-IgA

                    R2     p   n    country week full           outcome
IND_BM1      0.5684348 0.150 272        IND    1    1 RV-IgA (post-ORV)
IND_BM2      0.4020393 0.412 245        IND    7    1 RV-IgA (post-ORV)
IND_BM3      0.8380610 0.046 230        IND   11    1 RV-IgA (post-ORV)
MLW_BM1      0.7861263 0.846  80        MLW    1    1 RV-IgA (post-ORV)
MLW_BM2      1.9625820 0.160  70        MLW    7    1 RV-IgA (post-ORV)
MLW_BM3      0.6061001 0.960  67        MLW   11    1 RV-IgA (post-ORV)
UK_BM1       3.2182804 0.197  45         UK    1    1 RV-IgA (post-ORV)
UK_BM2       5.5700825 0.064  37         UK    7    1 RV-IgA (post-ORV)
UK_BM3       1.4027478 0.839  36         UK   11    1 RV-IgA (post-ORV)
INDexp_BM1   0.3493443 0.852 149 IND (neo+)    1    0 RV-IgA (post-ORV)
INDexp_BM2   0.4653291 0.809 132 IND (neo+)    7    0 RV-IgA (post-ORV)
INDexp_BM3   1.0262361 0.239 126 IND (neo+)   11    0 RV-IgA (post-ORV)
INDunexp_BM1 3.3948972 0.002 122 IND (neo-)    1    0 RV-IgA (post-ORV)
INDunexp_BM2 0.6083572 0.762 112 IND (neo-)    7    0 RV-IgA (post-ORV)
INDunexp_BM3 0.6870211 0.734 103 IND (neo-)   11    0 RV-IgA (post-ORV)

Dose 1 shedding

                    R2     p   n    country week full         outcome
IND_BM1      0.2283407 0.757 272        IND    1    1 dose 1 shedding
IND_BM2      0.5387310 0.186 245        IND    7    1 dose 1 shedding
MLW_BM1      1.3435442 0.383  77        MLW    1    1 dose 1 shedding
MLW_BM2      1.4937325 0.442  67        MLW    7    1 dose 1 shedding
INDexp_BM1   0.3806246 0.811 147 IND (neo+)    1    0 dose 1 shedding
INDexp_BM2   0.8939386 0.277 130 IND (neo+)    7    0 dose 1 shedding
INDunexp_BM1 0.7639850 0.456 122 IND (neo-)    1    0 dose 1 shedding
INDunexp_BM2 0.7878907 0.513 112 IND (neo-)    7    0 dose 1 shedding

Differential taxa

Column

Seroconversion

Genus- and RSV-level models

Summary plot

Differential genera - Fisher’s test or Aldex2 (FDR p <0.05)

Differential RSVs - Fisher’s test or Aldex2 (FDR p <0.05)

RV-IgA

Genus- and RSV-level models

Summary plot

Differential genera - Fisher’s test or Aldex2 (FDR p <0.05)

Differential RSVs - Fisher’s test or Aldex2 (FDR p <0.05)

Dose 1 shedding

Genus- and RSV-level models

Summary plot

Differential genera - Fisher’s test or Aldex2 (FDR p <0.05)

Differential RSVs - Fisher’s test or Aldex2 (FDR p <0.05)

Summary figures

Seroconversion

RV-IgA

Dose 1 shedding

Longitudinal abundance comparisons

Immunogenicity

Number of infants/taxa included in longitudinal models:

  • India (full), n infants: 300; n samples: 747; n taxa: 53
  • India (exposed), n infants: 164; n samples: 407; n taxa: 56
  • India (unexposed), n infants: 135; n samples: 337; n taxa: 49
  • Malawi, n infants: 97; n samples: 217; n taxa: 50
  • UK, n infants: 43; n samples: 109; n taxa: 31

India

          
           negatively correlated ns positively correlated
  age                          6  5                    42
  IgA                          0 53                     0
  seroconv                     0 53                     0
                                                taxon Estimate Std.Error
1                                     Bifidobacterium    0.032     0.010
2                                       Streptococcus    0.027     0.006
3                                      Staphylococcus   -0.131     0.008
4                                         Veillonella    0.179     0.009
5                                       Lactobacillus    0.111     0.010
6                                         Collinsella    0.045     0.008
7                                         Haemophilus   -0.035     0.008
8                                          Klebsiella   -0.092     0.009
10                                             Rothia    0.019     0.009
11                                            Gemella   -0.052     0.008
12                                           Bacillus    0.061     0.009
13                                        Pseudomonas    0.036     0.009
14                                      Cutibacterium    0.078     0.009
15                                       Enterobacter   -0.043     0.007
16                                      Acinetobacter    0.026     0.011
17                                      Enhydrobacter    0.075     0.008
19                                    Hydrogenophilus    0.128     0.009
20                                     Bradyrhizobium    0.070     0.009
21                                        Dermacoccus    0.023     0.008
22                                         Paracoccus    0.052     0.009
23                                     Granulicatella    0.104     0.008
24                                        Micrococcus    0.070     0.008
25                                            Kocuria    0.080     0.008
26                                                S31    0.141     0.009
27                                         Janibacter    0.052     0.008
28                                          Aeromonas    0.068     0.009
29                                         Aerococcus    0.039     0.007
30                                         Shewanella    0.086     0.008
31                                   Chryseobacterium    0.055     0.008
32                                    Cloacibacterium    0.113     0.008
34                                    Exiguobacterium    0.080     0.008
36                                      Alishewanella    0.021     0.009
37                                    Brachybacterium    0.043     0.008
38                                   Rubellimicrobium    0.068     0.009
39                                      Brevundimonas    0.086     0.009
40                                   Stenotrophomonas    0.057     0.008
41                                        Geobacillus    0.103     0.009
42                                         Bergeyella    0.025     0.007
43                                          Moraxella    0.039     0.008
44                                  Saccharopolyspora    0.058     0.009
45                                       Anaerococcus    0.020     0.009
47 Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium    0.046     0.008
48                                       Qipengyuania    0.095     0.010
49                                     Brevibacterium    0.052     0.008
50                                 Ornithinimicrobium    0.090     0.009
51                                        Deinococcus    0.112     0.001
52                                         unassigned   -0.070     0.009
53                                       Sphingomonas    0.132     0.009
            padj comparison
1   9.367442e-04        age
2   1.209487e-05        age
3   5.123333e-45        age
4   8.480000e-61        age
5   5.300000e-23        age
6   2.005405e-07        age
7   2.252500e-05        age
8   5.653333e-20        age
10  3.157447e-02        age
11  1.519333e-09        age
12  7.746154e-12        age
13  2.068293e-04        age
14  2.090556e-17        age
15  1.026875e-08        age
16  2.765217e-02        age
17  2.789474e-17        age
19  6.738571e-36        age
20  4.795238e-15        age
21  3.734091e-03        age
22  3.273529e-08        age
23  1.855000e-29        age
24  2.040500e-16        age
25  4.858333e-22        age
26  5.167500e-42        age
27  5.110714e-11        age
28  2.312727e-14        age
29  4.391429e-08        age
30  2.544000e-24        age
31  3.729630e-11        age
32  1.855000e-36        age
34  1.514286e-21        age
36  1.531111e-02        age
37  5.741667e-08        age
38  3.312500e-12        age
39  1.309412e-19        age
40  7.746154e-12        age
41  9.422222e-26        age
42  6.309524e-04        age
43  6.973684e-06        age
44  8.955172e-11        age
45  3.312500e-02        age
47  1.043939e-08        age
48  9.606250e-20        age
49  1.538710e-09        age
50  1.514286e-21        age
51 3.869000e-276        age
52  3.686957e-14        age
53  7.314000e-41        age

Summary statistics

[1] "No significant differences according to ORV outcome"

India (exposed)

          
           negatively correlated ns positively correlated
  age                          8 11                    37
  IgA                          0 56                     0
  seroconv                     0 56                     0
                                                taxon Estimate Std.Error
2                                       Streptococcus    0.038     0.008
3                                      Staphylococcus   -0.128     0.011
4                                         Veillonella    0.193     0.012
5                                       Lactobacillus    0.097     0.015
7                                         Haemophilus   -0.037     0.013
8                                          Klebsiella   -0.067     0.013
10                                             Rothia    0.032     0.011
11                                            Gemella   -0.082     0.009
12                                           Bacillus    0.066     0.012
13                                        Pseudomonas    0.028     0.012
14                                      Cutibacterium    0.059     0.012
15                                       Enterobacter   -0.035     0.010
17                                      Enhydrobacter    0.095     0.011
18                                  Corynebacterium_1    0.027     0.011
19                                    Hydrogenophilus    0.149     0.012
20                                     Bradyrhizobium    0.088     0.012
21                                            Blautia   -0.025     0.012
22                                        Dermacoccus    0.059     0.012
23                                         Paracoccus    0.056     0.013
24                                     Granulicatella    0.159     0.009
25                                        Micrococcus    0.080     0.011
26                                            Kocuria    0.068     0.010
27                                                S31    0.125     0.014
29                                          Aeromonas    0.032     0.011
30                                         Aerococcus    0.067     0.010
31                                         Shewanella    0.041     0.010
32                                   Chryseobacterium    0.039     0.012
33                                    Cloacibacterium    0.101     0.012
34                                       Rheinheimera    0.050     0.011
35                                    Exiguobacterium    0.085     0.011
38                                    Brachybacterium    0.035     0.011
39                                   Rubellimicrobium    0.114     0.014
40                                      Brevundimonas    0.103     0.012
41                                   Stenotrophomonas    0.076     0.018
42                                        Geobacillus    0.059     0.018
43                                         Bergeyella    0.045     0.010
45                                          Neisseria   -0.027     0.012
46                                  Saccharopolyspora    0.144     0.011
47                                       Anaerococcus   -0.025     0.012
49 Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium    0.038     0.011
50                                       Qipengyuania    0.095     0.014
52                                 Ornithinimicrobium    0.094     0.012
53                                        Deinococcus    0.063     0.002
54                                    Novosphingobium    0.058     0.010
56                                       Sphingomonas    0.127     0.014
           padj comparison
2  6.844444e-06        age
3  7.653333e-25        age
4  4.106667e-37        age
5  5.333333e-10        age
7  5.887179e-03        age
8  2.464000e-06        age
10 6.160000e-03        age
11 3.304000e-15        age
12 2.678261e-07        age
13 3.255814e-02        age
14 1.330000e-06        age
15 1.218824e-03        age
17 1.773333e-14        age
18 2.048780e-02        age
19 4.144000e-25        age
20 3.325000e-11        age
21 4.106667e-02        age
22 6.030769e-06        age
23 4.666667e-05        age
24 5.320000e-42        age
25 7.155556e-11        age
26 8.252632e-11        age
27 1.400000e-16        age
29 5.010526e-03        age
30 4.941176e-11        age
31 1.417500e-04        age
32 2.333333e-03        age
33 3.304000e-15        age
34 1.980000e-05        age
35 1.082667e-11        age
38 3.935135e-03        age
39 1.680000e-14        age
40 2.153846e-14        age
41 5.419355e-05        age
42 1.392000e-03        age
43 4.055172e-05        age
45 3.255814e-02        age
46 9.520000e-31        age
47 4.106667e-02        age
49 8.993939e-04        age
50 4.760000e-10        age
52 3.160000e-13        age
53 8.960000e-74        age
54 2.240000e-08        age
56 1.400000e-16        age

Summary statistics

[1] "No significant differences according to ORV outcome"

India (unexposed)

          
           negatively correlated ns positively correlated
  age                          5  9                    35
  IgA                          0 49                     0
  seroconv                     0 49                     0
                taxon Estimate Std.Error         padj comparison
1     Bifidobacterium    0.058     0.014 1.102500e-04        age
3      Staphylococcus   -0.139     0.012 4.704000e-22        age
4         Veillonella    0.166     0.014 7.840000e-25        age
5       Lactobacillus    0.158     0.016 5.390000e-18        age
6         Collinsella    0.078     0.013 1.653750e-08        age
7         Haemophilus    0.046     0.010 6.533333e-06        age
8          Klebsiella   -0.163     0.013 3.332000e-25        age
10            Gemella   -0.061     0.013 7.669565e-06        age
11           Bacillus    0.053     0.012 2.744000e-05        age
12        Pseudomonas    0.046     0.015 2.994444e-03        age
13      Cutibacterium    0.103     0.013 6.236364e-13        age
14      Acinetobacter    0.055     0.014 1.738710e-04        age
15      Enhydrobacter    0.039     0.013 3.840541e-03        age
17    Hydrogenophilus    0.095     0.013 7.513333e-11        age
19         Paracoccus    0.048     0.013 3.891176e-04        age
20     Granulicatella    0.058     0.013 2.654167e-05        age
21        Micrococcus    0.058     0.012 2.836842e-06        age
22            Kocuria    0.091     0.012 1.820000e-11        age
23                S31    0.111     0.012 2.123333e-15        age
25          Aeromonas    0.119     0.014 3.969000e-15        age
26         Shewanella    0.067     0.015 3.580769e-05        age
27   Chryseobacterium    0.064     0.011 9.511765e-08        age
28    Cloacibacterium    0.127     0.012 8.166667e-21        age
30    Exiguobacterium    0.037     0.013 6.247500e-03        age
31      Alishewanella    0.068     0.013 9.800000e-07        age
32    Brachybacterium    0.056     0.012 6.533333e-06        age
34      Brevundimonas    0.053     0.014 2.143750e-04        age
35   Stenotrophomonas    0.046     0.012 3.266667e-04        age
37          Moraxella    0.049     0.014 5.320000e-04        age
38  Saccharopolyspora   -0.036     0.012 3.868421e-03        age
39       Anaerococcus    0.056     0.014 1.738710e-04        age
40          Comamonas    0.056     0.012 7.669565e-06        age
41           Massilia    0.064     0.016 1.016296e-04        age
43   Chryseomicrobium    0.029     0.010 5.402564e-03        age
44       Qipengyuania    0.103     0.010 5.390000e-18        age
45     Brevibacterium    0.097     0.013 9.800000e-12        age
46 Ornithinimicrobium    0.053     0.013 1.605172e-04        age
47        Deinococcus    0.088     0.012 1.820000e-11        age
48         unassigned   -0.137     0.012 4.287500e-22        age
49       Sphingomonas    0.140     0.012 2.776667e-23        age

Summary statistics

[1] "No significant differences according to ORV outcome"

Malawi

          
           negatively correlated ns positively correlated
  age                         10 20                    20
  IgA                          0 49                     0
  seroconv                     1 49                     0
              taxon Estimate Std.Error         padj comparison
2     Streptococcus    0.058     0.010 1.500000e-07        age
3    Staphylococcus   -0.122     0.018 1.550000e-09        age
4       Bacteroides    0.041     0.017 2.833333e-02        age
5       Veillonella    0.119     0.018 3.181818e-09        age
6     Lactobacillus    0.163     0.019 9.166667e-13        age
8       Haemophilus   -0.046     0.013 9.782609e-04        age
9        Klebsiella   -0.118     0.018 1.269231e-08        age
10           Rothia    0.185     0.017 6.875000e-18        age
13         Bacillus   -0.117     0.010 1.350000e-20        age
17     Enterobacter   -0.184     0.017 4.333333e-18        age
19    Enhydrobacter    0.079     0.017 2.394737e-05        age
21     Agathobacter    0.072     0.016 2.750000e-05        age
23  Subdoligranulum   -0.072     0.024 5.384615e-03        age
24    Succinivibrio   -0.105     0.015 6.062500e-10        age
26   Ruminococcus_2   -0.074     0.016 3.571429e-05        age
27            Dorea    0.089     0.015 1.062500e-07        age
31          Kocuria    0.092     0.018 2.111111e-06        age
33       Janibacter    0.046     0.016 1.107143e-02        age
34        Aeromonas    0.138     0.013 5.100000e-17        age
35     Prevotella_7    0.122     0.017 2.571429e-10        age
37      Actinomyces    0.073     0.025 7.407407e-03        age
38  Brachybacterium    0.045     0.018 2.413793e-02        age
39    Brevundimonas    0.113     0.018 2.178571e-08        age
41 Stenotrophomonas    0.051     0.013 2.954545e-04        age
42       Bergeyella   -0.044     0.013 2.291667e-03        age
44      Citricoccus    0.088     0.014 9.166667e-09        age
45 Methylobacterium    0.055     0.017 2.800000e-03        age
46   Brevibacterium    0.097     0.016 1.033333e-07        age
47     Empedobacter   -0.230     0.010 6.500000e-43        age
48          Dietzia    0.167     0.024 1.111111e-09        age
82   Alloprevotella   -1.505     0.414 2.250000e-02   seroconv

Summary statistics

            taxon Estimate Std.Error   padj comparison  mean prev
82 Alloprevotella   -1.505     0.414 0.0225   seroconv 0.254   23

UK

          
           negatively correlated ns positively correlated
  age                         10  9                    12
  IgA                          0 30                     0
  seroconv                     0 30                     0
                                                taxon Estimate Std.Error
1                                     Bifidobacterium    0.047     0.021
3                                      Staphylococcus   -0.102     0.016
4                                         Bacteroides    0.124     0.019
7                                         Haemophilus   -0.058     0.018
8                                          Klebsiella    0.114     0.020
9                                              Rothia    0.144     0.018
10                                            Gemella   -0.106     0.018
11                                        Pseudomonas    0.142     0.023
13                                       Enterobacter   -0.101     0.026
15                                      Enhydrobacter    0.157     0.024
17                                        Dermacoccus    0.070     0.015
18                                     Granulicatella    0.119     0.023
19                                        Micrococcus    0.039     0.018
20                                            Kocuria   -0.226     0.025
21                                   Chryseobacterium   -0.218     0.029
24                                         Lawsonella    0.058     0.015
26                                          Moraxella   -0.064     0.018
27                                          Neisseria   -0.098     0.021
28                                        Lactococcus    0.101     0.018
29 Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium   -0.071     0.026
30                                         unassigned   -0.125     0.012
31                                       Sphingomonas    0.104     0.025
           padj comparison
1  4.790909e-02        age
3  1.860000e-07        age
4  6.716667e-08        age
7  2.936842e-03        age
8  6.200000e-07        age
9  4.650000e-10        age
10 7.130000e-07        age
11 1.860000e-07        age
13 4.456250e-04        age
15 4.836000e-08        age
17 2.623077e-05        age
18 5.425000e-06        age
19 4.790909e-02        age
20 1.209000e-11        age
21 2.015000e-09        age
24 4.558824e-04        age
26 9.644444e-04        age
27 3.764286e-05        age
28 2.282727e-06        age
29 1.410500e-02        age
30 2.294000e-14        age
31 1.570667e-04        age

Summary statistics

[1] "No significant differences according to ORV outcome"

Dose 1 shedding

Number of infants/taxa included in longitudinal models:

  • India (full), n infants: 296; n samples: 517; n taxa: 53
  • India (exposed), n infants: 160; n samples: 277; n taxa: 57
  • India (unexposed), n infants: 133; n samples: 234; n taxa: 52
  • Malawi, n infants: 88; n samples: 144; n taxa: 51
  • UK, n infants: 51; n samples: 89; n taxa: 33

India

                
                 ns positively correlated
  dose1_shedding 51                     2

Summary statistics

             taxon Estimate Std.Error     padj     comparison  mean prev
19 Hydrogenophilus    0.662     0.198 0.024645 dose1_shedding 0.836 52.0
46        Massilia    1.124     0.278 0.003604 dose1_shedding 0.247 21.3

India (exposed)

                
                 ns
  dose1_shedding 57

Summary statistics

[1] "No significant differences according to ORV outcome"

India (unexposed)

                
                 ns positively correlated
  dose1_shedding 51                     1

Summary statistics

      taxon Estimate Std.Error      padj     comparison  mean prev
44 Massilia    1.623     0.328 0.0001196 dose1_shedding 0.399 25.2

Malawi

                
                 ns
  dose1_shedding 51

Summary statistics

[1] "No significant differences according to ORV outcome"

.

Session info

R version 4.1.2 (2021-11-01)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur 10.16

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib

locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets 
[8] methods   base     

other attached packages:
 [1] FSA_0.9.1                   ALDEx2_1.26.0              
 [3] zCompositions_1.4.0         truncnorm_1.0-8            
 [5] NADA_1.6-1.1                survival_3.2-13            
 [7] MASS_7.3-55                 sjstats_0.18.0             
 [9] ggExtra_0.9                 formattable_0.2.1          
[11] NBZIMM_1.0                  inlmisc_0.5.2              
[13] decontam_1.14.0             ggtree_3.2.1               
[15] wesanderson_0.3.6           phangorn_2.8.1             
[17] ape_5.6-1                   DECIPHER_2.22.0            
[19] RSQLite_2.2.9               Biostrings_2.62.0          
[21] XVector_0.34.0              cowplot_1.1.1              
[23] scales_1.1.1                RVAideMemoire_0.9-81       
[25] DescTools_0.99.44           ggsignif_0.6.3             
[27] binom_1.1-1                 shiny_1.7.1                
[29] randomcoloR_1.1.0.1         DESeq2_1.34.0              
[31] SummarizedExperiment_1.24.0 Biobase_2.54.0             
[33] MatrixGenerics_1.6.0        GenomicRanges_1.46.1       
[35] GenomeInfoDb_1.30.0         IRanges_2.28.0             
[37] S4Vectors_0.32.3            BiocGenerics_0.40.0        
[39] crossval_1.0.4              UpSetR_1.4.0               
[41] labdsv_2.0-1                mgcv_1.8-38                
[43] nlme_3.1-155                ggpubr_0.4.0               
[45] data.table_1.14.2           corrplot_0.92              
[47] ZIBR_0.1                    vegan_2.5-7                
[49] lattice_0.20-45             permute_0.9-7              
[51] randomForest_4.6-14         matrixStats_0.61.0         
[53] lme4_1.1-27.1               Matrix_1.4-0               
[55] reshape2_1.4.4              pheatmap_1.0.12            
[57] DT_0.20                     plotly_4.10.0              
[59] cluster_2.1.2               tidyr_1.1.4                
[61] dplyr_1.0.7                 magrittr_2.0.1             
[63] plyr_1.8.6                  kableExtra_1.3.4           
[65] gridExtra_2.3               RColorBrewer_1.1-2         
[67] knitr_1.37                  ggplot2_3.3.5              
[69] phyloseq_1.38.0            

loaded via a namespace (and not attached):
  [1] estimability_1.3       coda_0.19-4            bit64_4.0.5           
  [4] DelayedArray_0.20.0    KEGGREST_1.34.0        RCurl_1.98-1.5        
  [7] generics_0.1.1         terra_1.5-12           proxy_0.4-26          
 [10] bit_4.0.4              webshot_0.5.2          xml2_1.3.3            
 [13] httpuv_1.6.5           assertthat_0.2.1       xfun_0.29             
 [16] hms_1.1.1              jquerylib_0.1.4        evaluate_0.14         
 [19] promises_1.2.0.1       fansi_1.0.2            igraph_1.2.11         
 [22] DBI_1.1.2              geneplotter_1.72.0     htmlwidgets_1.5.4     
 [25] purrr_0.3.4            ellipsis_0.3.2         backports_1.4.1       
 [28] V8_4.0.0               insight_0.15.0         annotate_1.72.0       
 [31] vctrs_0.3.8            sjlabelled_1.1.8       abind_1.4-5           
 [34] cachem_1.0.6           withr_2.4.3            rgdal_1.5-28          
 [37] emmeans_1.7.2          treeio_1.18.1          svglite_2.0.0         
 [40] lazyeval_0.2.2         crayon_1.4.2           flexdashboard_0.5.2   
 [43] genefilter_1.76.0      labeling_0.4.2         pkgconfig_2.0.3       
 [46] rlang_0.4.12           lifecycle_1.0.1        miniUI_0.1.1.1        
 [49] modelr_0.1.8           datawizard_0.2.2       aplot_0.1.2           
 [52] raster_3.5-11          carData_3.0-5          Rhdf5lib_1.16.0       
 [55] boot_1.3-28            png_0.1-7              viridisLite_0.4.0     
 [58] parameters_0.16.0      rootSolve_1.8.2.3      bitops_1.0-7          
 [61] rhdf5filters_1.6.0     blob_1.2.2             stringr_1.4.0         
 [64] rstatix_0.7.0          gridGraphics_0.5-1     memoise_2.0.1         
 [67] zlibbioc_1.40.0        compiler_4.1.2         ade4_1.7-18           
 [70] patchwork_1.1.1        tidyselect_1.1.1       forcats_0.5.1         
 [73] stringi_1.7.6          highr_0.9              yaml_2.2.1            
 [76] locfit_1.5-9.4         grid_4.1.2             sass_0.4.0            
 [79] fastmatch_1.1-3        tools_4.1.2            lmom_2.8              
 [82] rstudioapi_0.13        foreach_1.5.1          gld_2.6.4             
 [85] farver_2.1.0           Rtsne_0.15             RcppZiggurat_0.1.6    
 [88] digest_0.6.29          quadprog_1.5-8         Rcpp_1.0.8            
 [91] car_3.0-12             broom_0.7.11           performance_0.8.0     
 [94] later_1.3.0            httr_1.4.2             AnnotationDbi_1.56.2  
 [97] effectsize_0.6.0       colorspace_2.0-2       rvest_1.0.2           
[100] XML_3.99-0.8           splines_4.1.2          yulab.utils_0.0.4     
[103] tidytree_0.3.7         expm_0.999-6           sp_1.4-6              
[106] multtest_2.50.0        Exact_3.1              ggplotify_0.1.0       
[109] systemfonts_1.0.2      xtable_1.8-4           jsonlite_1.7.3        
[112] nloptr_1.2.2.3         Rfast_2.0.4            ggfun_0.0.5           
[115] R6_2.5.1               pillar_1.6.4           htmltools_0.5.2       
[118] mime_0.12              glue_1.6.0             fastmap_1.1.0         
[121] minqa_1.2.4            BiocParallel_1.28.3    class_7.3-20          
[124] codetools_0.2-18       mvtnorm_1.1-3          utf8_1.2.2            
[127] bslib_0.3.1            tibble_3.1.6           curl_4.3.2            
[130] rmarkdown_2.11         biomformat_1.22.0      munsell_0.5.0         
[133] e1071_1.7-9            rhdf5_2.38.0           GenomeInfoDbData_1.2.7
[136] iterators_1.0.13       haven_2.4.3            sjmisc_2.8.9          
[139] gtable_0.3.0           bayestestR_0.11.5     

.